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1. Clc sequence viewer alignment export full#
2. Clc sequence viewer alignment export plus#
3. Clc sequence viewer alignment export download#

Output options, select create full contigs, including trace data.You can increase or decrease the alignment options to change the stringency of the alignment.Ĭonflict can be voted on (A, C, G, T), Assigned degenerate bases or assigned an N for ambiguous base when conflicts arise in the overlapping regions where the forward and reverse strand have different bases at the same position. Click next, this dialogue box allows one to define assembly parameters see Figure 7 below.This gives a dialogue box on the left panel select the forward and reverse sequences you want to assemble and move them to the right panel. Toolbox | Sequencing Data Analysis | Assemble sequences De novo assembly: common in the cases that you do not have a reference sequence to the sequenced data.Comparison with a similar sequence obtained from a sequence database Or Assembly can be done to a reference sequence.Assembling the two sequences aligns the sequences where they overlap to get a contiguous sequence called a contig. Assemble sequences: In most cases forward and reverse primers are used, hence on sequencing you end up with a forward and reverse sequence.These annotated sections are ignored in further analysis. When the trimming is done the parts of the sequences that are trimmed are not actually removed but trim annotations are saved to the sequences. Click next and choose to save the results.If the sequences were cloned products select the vector trimming options.Specify the trimming parameters the limit on trim quality scores can be increased or reduced to make trimming more or less stringent respectively.Select all the sequences to be trimmed on the left panel and use the arrow to move them to the right panel, click next.This gives the trim sequences dialogue box. Sequencing Data Analysis | Trim Sequences Trimming eliminates reads of poor quality (and in the case of cloned inserts removal of vector contamination). Trimming the sequences: The first step when analyzing the sequencing reads is to trim them.Your imported sequences should look as below Figure 3.įig 3 Assembling sequences: trimming, conflicts, consensus Double click the sequence in the Navigation area to view it Figure 3.The data is imported into CLC if you expand My_folder in the navigation area you should see your sequences.Select the folder to save the sequences to in CLC- in this case highlight My_folder and click finish.Select all the sequences you want to import (to import them concurrently) and click next.In the case of sequenced data select Trace files (.abi/.ab1/.scf/.phd). Navigate to where your sequences are stored on your computer.You can import many file types but in this tutorial we will look at importing trace files for further analysis.įile | import or click the import icon on the tool bar. Importing data: Allows you to bring sequenced data into CLC from where it is stored on your computer.Name the folder “My_folder” or a name of your choice and press enter. click on the new folder icon on the tool bar.Creating a folder, it is best to organize data in the navigation area in folders.View area is the main window to the right, where data is viewed and manipulated.Navigation area is where all the data imported into CLC is kept.The user interface of CLC is as below: there is Navigation area and a View area.

Clc sequence viewer alignment export download#

Clc sequence viewer alignment export plus#

It consists of a multiple sequence alignment of sequence reads plus a consensus sequence.Ĭonsensus sequence: A sequence of nucleotides in common between regions of homology in related DNA sequences. This can be more difficult if the region of overlap is very small.Ĭonflict: a nucleotide position in the assembled sequence overlap which has different bases, or where there is a gap on one sequence and a base at the corresponding position on the other sequence.ĭNA Contig: Contiguous sequence of DNA created by assembling overlapping DNA sequence reads. Sequence assembly: aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence.Īssembly to a reference sequence: assembly of the sequenced fragments using a similar sequence (a reference sequence) as a guide.ĭe novo assembly: assembly using only your sequenced fragments.